Pentachlorophenol (PCP) is a legacy persistent organic pollutant posing continuous threats to aquatic ecosystems. In this study, the systemic toxic mechanisms of PCP in zebrafish were investigated using a comprehensive toxico-multi-omics approach, integrating targeted metabolomics (GC-MS/MS) and proteomics (LC-Orbitrap-MS/MS). Zebrafish were exposed to PCP for 48 h in three groups: control (no exposure), low exposure (1/10 LC50), and high exposure (LC50). Integrative analysis identified 75 metabolomic and 376 proteomic biomarkers, revealing severe perturbations in interconnected pathways, including the pentose phosphate pathway and multiple amino acid metabolisms. Notably, the downregulation of crucial proteins (echs1 and hibch) and metabolites (N-acetyl aspartate) reflected a coordinated disruption of valine/branched-chain amino acid catabolism and mitochondrial energy metabolism, supported by concordant protein and metabolite changes. Furthermore, significantly elevated malondialdehyde levels confirmed structural cellular damage, while robust compensatory activations in innate defense mechanisms, specifically taurine and glucuronate metabolisms, were elucidated. Collectively, this integrated multi-omics investigation provides unprecedented mechanistic insights into the intricate interplay between PCP-induced metabolic and redox disruptions and the compensatory cellular defense systems in aquatic organisms.